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2014 International Year of

Celebrating

Myoglobin was the first visualized in three dimensions at the atomic level by X-ray crystallography, laying the foundation for a new era of biological understanding. For this discovery, and shared the 1962 in . In 1959 Max Perutz, whose methodological work had been crucial to Kendrew's success, determined the structure of , a protein closely related to myoglobin and the second to be analyzed by X-ray crystallography. January 2014

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IYCr Opening Ceremony in IYCr Opening Ceremony in Paris, France Paris, France 26 27 28 29 30 31 Ribosome

Ribosomes are complex molecular machines that serve as the primary site of biological protein synthesis. They are composed of two independent subunits of unequal size, which associate upon initiation of protein biosynthesis. Due to their enormous size, tendency to deteriorate, and functional heterogeneity, ribosomes are extremely challenging to crystallize.

For determining the detailed structure and mechanism of the ribosome Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath were jointly awarded the in 2009. February 2014

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23 24 25 26 27 28 Photosynthetic Reaction Center

The photosynthetic reaction center (PRC) is a complex of several , chlorophyll, and other cofactors assembled to execute the primary energy conversion reactions of . The PRC from the purple bacterium Rhodopseudomonas viridis was fundamental to our understanding of the structure and chemistry of this critical biological process. Its X-ray crystal structure was determined in 1982 by , and , for which they shared the Nobel Prize in Chemistry in 1988. PRC represented the first structure of an integral membrane protein. March 2014

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30 31 Daylight Saving Time begins (Europe) TATA-binding protein (top center) acutely bends its cognate DNA binding Protein-DNA sites, while other DNA-binding proteins deform their DNA binding sites to varying degrees (clockwise from top right: E2 protein, catabolite activator protein, resolvase, nucleosome core particle, integration host faγcδtor, SceI endonuclease, trp repressor). Complexes Background: X-ray diffraction image recorded by oscillation photography from a trp repressor crystal. April 2014

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Earth Day DNA Day 27 28 29 30 Aquaporin

Two-dimensional crystals consist of a single layer of molecules arranged in an ordered array. They are particularly useful for studying proteins embedded in lipid bilayer membranes, like those found in eukaryotic and bacterial walls. Electron diffraction, rather than X-ray diffraction, is the most effective tool for studying such systems at the atomic level. Yoshinori Fujiyoshi has designed a series of cryo-electron microscopes for this purpose and determined several important structures, including aquaporin 4, a channel that selectively con - ducts water across the cell wall. May 2014

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American Crystallographic Association (ACA) Meeting begins in Albuquerque, NM, USA 25 26 27 28 29 30 31

ACA Meeting ends Calcium Pump

E1•2Ca 2+ cytoplasm cytoplasm membrane E1•AIF 4-•ADP To activate muscle contraction, membrane nerve excitation releases a flood of calcium ions from a special intracellular compartment, known cytoplasm E1•Mg 2+ as the sarcoplasmic reticulum. The Ca 2+ 2+ 2+ 2+ calcium rapidly spreads throughout the membrane Ca E1•2Ca E1•2Ca •ATP muscle cell and binds to troponin, an integral ATP E1 P•2Ca 2+ •ADP ˜ component of thin filaments, producing a E1•Mg 2+ Mg 2+ conformational change that allows myosin ADP motors to climb up the thin filaments. Trillions of myosin motors continue

Mg 2+ climbing until the calcium is removed. nH+ 2+ 2Ca 2+ E1P[2Ca ] Calcium pumps in the membrane of the sarcoplasmic reticulum stop this frenetic Pi calcium-induced contraction. Powered by E2 nH + ATP, they pump calcium ions back into the E2•Pi E2P sarcoplasmic reticulum, which reduces the calcium level inside muscle cells leading to relaxation.

cytoplasm E2 Crystallographic studies by Chikashi membrane Toyoshima and colleagues inspired the structural model of the calcium ATPase pump cycle shown here. - cytoplasm E2•BeF 3

2- cytoplasm membrane E2•MgF 4

membrane June 2014

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25 26 27 28 29 30 31 27 28 29 30 31 Protein-Drug Complexes

Crystallography plays a central role in drug discovery by providing atomic level visualization of key protein-drug interactions. Abl tyrosine-kinase inhibitors have revolutionized treatment of chronic myeloid leukemia, which was typically fatal within a few years of diagnosis. Shown here is the structure of the Abl kinase bound to a first-generation drug, imatinib (orange), which inspired medicinal to design an even more effective second-generation treatment, nilotinib (green). The majority of patients treated with these drugs live for at least a decade. While imatinib and nilotinib are very similar in structure, nilotinib is less vulnerable to the emergence of drug resistance, as it makes a better fit to the enzyme active site. July 2014

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27 28 29 30 31 Tobacco Tobacco mosaic virus (TMV), the first virus to be discovered, was purified by Wendell Stanley via crystallization. He demonstrated that the virus is primarily composed of protein. Others showed that TMV contains a single- stranded RNA genome. Prominent structural biologists (including Mosaic J. D. Bernal, , Ken Holmes, , Don Caspar, and Gerald Stubbs) used X-ray diffraction and electron microscopy to study TMV's 3D structure. The RNA strand (purple) is enveloped by a protective Virus coat of capsid proteins (pink) arranged in a cylinder. Stanley and John Northrop shared the 1946 Nobel Prize in Chemistry "for their preparation of enzymes and virus proteins in a pure form."

Detail shows Rosalind Franklin and Aaron Klug's TMV model, sculpted by John Ernest for the 1958 Brussels World Exhibition International Science Pavilion. August 2014

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31 Reverse Transcriptase

HIV (human immunodeficiency virus), the cause of Acquired Immune Deficiency Syndrome or AIDS, is composed of two RNA strands, 15 distinct viral proteins, and a few proteins derived from the last host cell it infected, all surrounded by a lipid bilayer membrane. Together, these molecules allow the virus to infect cells of the immune system, thereby disabling the cells and forcing them to build new copies of the virus. Reverse transcriptase, highlighted in the image above and to the left, makes a DNA copy of the HIV RNA genome. The large image shows the enzyme assembling a DNA strand (magenta) from the viral RNA (red). Thereafter, the same enzyme destroys the original viral RNA as it builds a matching second DNA strand. The new double-stranded DNA can then be used to make both viral proteins and viral RNAs, which assemble to form new viruses. One component of the multidrug regimen currently used to fight HIV infection blocks the action of reverse transcriptase. September 2014

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24 25 26 27 28 29 30 26 27 28 29 30 31 31 Insulin pioneered the use of X-ray diffraction for determining structures of biological molecules. Following her studies of penicillin (blue pill) and vitamin B12 (orange pill), she was awarded the Nobel Prize in Chemistry in 1964 for contributions to the development of crystallography. Hodgkin later determined the structure of insulin, the hormone that controls glucose levels in the blood and one of the earliest protein structures.

"I used to say the evening that I developed the first X-ray photograph I took of insulin in 1935 was the most exciting moment of my life. But the Saturday afternoon in late July 1969, when we realized that the electron density map was interpretable, runs that moment very close."

Dorothy Hodgkin October 2014

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Daylight Saving Time ends (Europe) Fluorescent Proteins

Green Fluorescent Proteins (GFP) are found in jellyfish. They absorb ultraviolet light and then emit lower-energy green light. Since GFP creates its own chromophore, the chemical group that produces color, it is a popular tool for genetic engineering. GFP is used as a tag for monitoring individual proteins in cells or even in the body, and for examining protein stability. The 2008 Nobel Prize in Chemistry was awarded jointly to , , and Roger Y. Tsien for the discovery and development of GFP.

Variants of GFP and its evolutionary relatives emit light of different colors, which allows tracking of multiple distinct proteins in a single cell. November 2014

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30 G Protein-Coupled Receptor

G protein-coupled receptors (GPCRs) form the largest family of human integral membrane proteins. They transmit cellular signals from outside the cell to the cytoplasm and eventually the nucleus. They respond variously to neurotransmitters , hormones, and light as shown here. GPCRs represent important targets for drugs; more than 50% of approved drugs work by modulating the action of one or more GPCRs.

The 2012 Nobel Prize in Chemistry was awarded jointly to Robert J. Lefkowitz and Brian K. Kobilka for studies of GPCRs. The PDB holds many GPCR structures, including Kobilka's groundbreaking structure of the 2 adrenergic receptor bound to a G protein heterotrimer shown to the left. β December 2014

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IYCr Ends 23 24 25 26 27 28 29 25 26 27 28 29 30 31 30 References and Acknowledgements

Front Cover: February: Ribosome PDB ID: 1j59 G. Parkinson, C. Wilson, A. Gunasekera, Y. W. Ebright, R. E. Ebright, H.M. Berman. (1996) Structure of PDB ID: 6ldh C. Abad-Zapatero, J. P. Griffith, J. L. Suss - PDB ID: 1fjg A. P. Carter, W. M. Clemons, D. E. Brodersen, the CAP-DNA complex at 2.5 Å resolution: a complete pic - man, M. G. Rossmann. (1987) Refined crystal structure of R. J. Morgan-Warren, B. T. Wimberly, V. Ramakrishnan. ture of the protein-DNA interface J.Mol.Biol. 260 : dogfish M4 apo-lactate dehydrogenase. J.Mol.Biol. 198 : (2000) Functional insights from the structure of the 30S 395-408. 445-467. ribosomal subunit and its interactions with antibiotics. Nature 407 : 340-348. PDB ID: 1aoi K. Luger, A. W. Mader, R. K. Richmond, D. F. PDB ID: 2cha J. J. Birktoft, D. M. Blow. (1972). Structure of PDB ID: 1fka F. Schluenzen, A. Tocilj, R. Zarivach, J. Harms, M. Gluehmann, D. Sargent, T. J. Richmond. (1997) Crystal structure of the nu - crystalline alpha-chymotrypsin. V. The atomic structure of Janell, A. Bashan, H. Bartels, I. Agmon, F. Franceschi, A. Yonath. (2000) cleosome core particle at 2.8Å resolution Nature 389 : tosyl-alpha-chymotrypsin at 2 Å resolution. J.Mol.Biol. 68 : Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. 251-260. 187-240. Cel l 102 : 615-623. PDB ID: 1ffk N. Ban, P. Nissen, J. Hansen, P. B. Moore, T. A. Steitz. (2000) PDB ID: 1gdt W. Yang, T. A. Steitz. (1995) Crystal PDB ID: 1cyo R. C. Durley, F. S. Mathews. (1996) Refine - The complete atomic structure of the large ribosomal subunit at a 2.4 Å reso - structure of the site-specific recombinase gamma delta ment and structural analysis of bovine cytochrome b5 at lution. Science 289 : 905-920. resolvase complexed with a 34 bp cleavage site Cell 82 : 1.5 Å resolution. Acta Crystallogr. ,Sect.D 52 : 65-76. 193-207. March: Photosynthetic Reaction Center PDB ID: 2np2 K. W. Mouw, P. A. Rice. (2007) Shaping the PDB ID: 4pti M. Marquart, J. Walter, J. Deisenhofer, W. PDB ID: 1prc J. Deisenhofer, O. Epp, I. Sinning, H. Michel. Borrelia burgdorferi genome: crystal structure and binding Bode, R. Huber. (1983) The geometry of the reactive site and (1995) Crystallographic refinement at 2.3 Å resolution and properties of the DNA-bending protein Hbb Mol.Microbiol. of the peptide groups in trypsin, trypsinogen and its com - refined model of the photosynthetic reaction centre from 63 : 1319-1330. plexes with inhibitors Acta Crystallogr. ,Sect.B 39 : 480-490. Rhodopseudomonas viridis. J.Mol.Biol. 246 : 429-457.

PDB ID: 3cpa D. W. Christianson, W. N. Lipscomb. (1986) April: Protein-DNA Complexes X-ray crystallographic investigation of substrate binding May: Aquaporin to carboxypeptidase A at subzero temperature. PDB ID: 1vtl J. L. Kim, D. B. Nikolov, S. K. Burley. (1993) PDB ID: 3iyz T. Mitsuma, K. Tani, Y. Hiroaki, A. Kamegawa, Proc.Natl.Acad.Sci.USA 83 : 7568-7572 Co-crystal structure of TBP recognizing the minor groove of H. Suzuki, H. Hibino, Y. Kurachi, Y. Fujiyoshi. (2010) Influ - a TATA element. Nature 365 : 520-527. ence of the cytoplasmic domains of aquaporin-4 on water PDB ID: 2lhb R. B. Honzatko, W. A. Hendrickson, W. E. conduction and array formation . J.Mol.Biol. 402 : 669-681 Love. (1985) Refinement of a for lamprey PDB ID: 1lws C. M. Moure, F. S. Gimble, F. A. Quiocho. hemoglobin from Petromyzon marinus. J.Mol.Biol. 184 : Photos courtesy of Professor Yoshinori Fujiyoshi (Nagoya University) (2002) Crystal structure of the intein homing endonuclease 147-164. Molecular image courtesy of Dr. Hirofumi Suzuki (Osaka University) PI-SceI bound to its recognition sequence Nat.Struct.Biol. 9: 764-770. PDB ID: 1sbt R. A. Alden, J. J. Birktoft, J. Kraut, June: Calcium Pump J. D. Robertus, C.S. Wright. (1971). Atomic coordinates for subtilisin BPN' (or Novo). Biochem.Biophys.Res.Commun. PDB ID: 1tro Z. Otwinowski, R. W. Schevitz, R.-G. Zhang, PDB ID: 3w5a C. Toyoshima, S. Iwasawa, H. Ogawa, 45 : 337-344. C. L. Lawson, A. Joachimiak, R. Q. Marmorstein, B. F. Luisi, A. Hirata, J. Tsueda, G. Inesi. (2013) Crystal structures of the P. B. Sigler. (1988) Crystal structure of trp repressor/ calcium pump and sarcolipin in the Mg 2+ -bound E1 state. operator complex at atomic resolution Nature 335 : 321-329. Nature 495 : 260-264. January: Myoglobin PDB ID: 1mbn J. C. Kendrew, G. Bodo, H. M. Dintzis, R. G. PDB ID: 2bop R. S. Hegde, S. R. Grossman, L. A. Laimins, PDB ID: 1su4 C. Toyoshima, M. Nakasako, H. Nomura, H. Parrish, H. Wyckoff, D. C. Phillips. (1958) A three-dimen - P. B. Sigler. (1992) Crystal structure at 1.7 Å of the bovine Ogawa. (2000) Crystal structure of the calcium pump of sional model of the myoglobin molecule obtained by X-ray papillomavirus-1 E2 DNA-binding domain bound to its sarcoplasmic reticulum at 2.6 Å resolution. Nature 405 : analysis. Nature 181 : 662-666. DNA target Nature 359 : 505-512. 647-655.

PDB ID: 2zbd C. Toyoshima, H. Nomura, T. Tsuda. (2004) September: Reverse Transcriptase Back Cover References Lumenal gating mechanism revealed in calcium pump PDB ID: 1hys S. G. Sarafianos, K. Das, C. Tantillo, A. D. 1. J. C. Kendrew, G. Bodo, H. M. Dintzis, et al. (1958) A three-dimensional crystal structures with phosphate analogues. Nature 432 : Clark, Jr., J. Ding, J. M. Whitcomb, P. L. Boyer, S. H. Hughes, model of the myoglobin molecule obtained by X-ray analysis. Nature 181 : 361-368. E. Arnold. (2001) Crystal structure of HIV-1 reverse tran - 662-666. scriptase in complex with a polypurine tract RNA:DNA. 2. J. C. Kendrew, R E. Dickerson, B. E. Strandberg, et al. (1960) Structure of PDB ID: 2zbe C. Toyoshima, Y. Norimatsu, S. Iwasawa, T. EMBO J. 20 : 1449-1461. Tsuda, H. Ogawa. (2007) How processing of aspartylphos - myoglobin: A three-dimensional Fourier synthesis at 2 Å. resolution. phate is coupled to lumenal gating of the ion pathway in October: Insulin Nature 185 : 422-427. the calcium pump. Proc.Natl.Acad.Sci.USA 104 : 19831- 3. M. F. Perutz, M. G. Rossmann, A. F. Cullis, et al . (1960) Structure of 19836. PDB ID: 4ins E. N. Baker, T. L. Blundell, J. F. Cutfield, S. M. Cutfield, E. J. Dodson, G. G. Dodson, D. M. Hodgkin, R. E. Hub - haemoglobin: a three-dimensional Fourier synthesis at 5.5 Å resolution, PDB ID: 1wpg C. Toyoshima, H. Nomura, T. Tsuda. (2004) bard, N. W. Isaacs, C. D. Reynolds, K. Sakabe, N. Sakabe, N. M. obtained by X-ray analysis. Nature 185 : 416-422. Lumenal gating mechanism revealed in calcium pump Vijayan. (1988) The structure of 2Zn pig insulin crystals at 1.5 4. W. Bolton, M. F. Perutz. (1970) Three dimensional fourier synthesis of crystal structures with phosphate analogues. Nature 432 : Å resolution. Philos.Trans.R.Soc.Lond.B.Biol.Sci . 319 : 369-456. 361-368. horse deoxyhaemoglobin at 2.8 Ångstrom units resolution. Nature 228 : 551-552. November: Fluorescent Proteins PDB ID: 3w5c C. Toyoshima, S. Iwasawa, H. Ogawa, 6. C. C. F. Blake, D.F. Koenig, G.A. Mair, et al. (1965) Structure of hen PDB ID: 1ema M. Ormo, A. B. Cubitt, K. Kallio, L. A. Gross, A. Hirata, J. Tsueda, G. Inesi. (2013) Crystal structures of the egg-white lysozyme. A three dimensional Fourier synthesis at 2 Å R. Y. Tsien, S. J. Remington. (1996) Crystal structure of the calcium pump and sarcolipin in the Mg 2+ -bound E1 state. resolution. Nature 206 : 757-761. Aequorea victoria green fluorescent protein. Science 273 : Nature 495 : 260-264. 1392-1395. 7. C. C. F. Blake, L. N. Johnson, G. A. Mair, et al. (1967) Crystallographic studies of the activity of hen egg-white lysozyme. Proc.R.Soc. Molecular images courtesy of Dr. Ryuta Kanai (University of Tokyo) Ser.B 167 : 378-388. Background photo courtesy of zcool.com.cn PDB ID: 1bfp R. M. Wachter, B. A. King, R. Heim, K. Kallio, R. Y. Tsien, S. G. Boxer, S. J. Remington. (1997) Crystal 8. G. Kartha, J. Bello, D. Harker. (1967) Tertiary structure of ribonuclease. July: Protein-Drug Complexes structure and photodynamic behavior of the blue emission Nature 213 : 862-865. PDB ID: 3cs9 E. Weisberg, P. W. Manley, W. Breitenstein, variant Y66H/Y145F of green fluorescent protein. Biochem - 9. H. W. Wyckoff, K. D. Hardman, N. M. Allewell, et al. (1967) The structure J. Bruggen, S. W. Cowan-Jacob, A. Ray, B. Huntly, D. Fab - istry 36 : 9759-9765. of ribonuclease-S at 6 Å resolution. J.Biol.Chem. 242 : 3749-3753. bro, G. Fendrich, E. Hall-Meyers, A. L. Kung, J. Mestan, G. Q. Daley, L. Callahan, L. Catley, C. Cavazza, M. Azam, D. PDB ID: 1yfp R. M. Wachter, M. A. Elsliger, K. Kallio, G. T. Molecular images were created using Chimera (E.F. Pettersen, T.D. Goddard, Neuberg, R. D. Wright, D. G. Gilliland, J. D. Griffin. (2005) Hanson, S. J. Remington. (1998) Structural basis of spectral C.C. Huang, et al. (2004) UCSF Chimera–a visualization system for exploratory Characterization of AMN107, a selective inhibitor of native shifts in the yellow-emission variants of green fluorescent research and analysis. J Comput Chem 25 : 1605-1612.), PyMOL (The PyMOL and mutant Bcr-Abl. Cancer Cell 7: 129-141. protein. Structure 6: 1267-1277. Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC.) and autoPACK PDB ID: 2hyy S. W. Cowan-Jacob, G. Fendrich, A. Floer - (Graham Johnson, Ludovic Autin, Mostafa Al-Alusi, David Goodsell, Michel sheimer, P. Furet, J. Liebetanz, G. Rummel, P. Rheinberger, M. PDB ID: 1g7k D. Yarbrough, R. M. Wachter, K. Kallio, M. Sanner and Art Olson; open-source at autopack.org ). Centeleghe, D. Fabbro, P. W. Manley. (2007) Structural biol - V. Matz, S. J. Remington. (2001) Refined crystal structure of ogy contributions to the discovery of drugs to treat chronic DsRed, a red fluorescent protein from coral, at 2.0-Å resolu - This calendar was developed by the wwPDB team, with special thanks to myelogenous leukaemia. Acta Crystallog. , Sect. D 63 : 80-93. tion. Proc.Nat.Acad.Sci.USA 98 : 462-467. Gary Battle (PDBe) and to Luigi Di Costanzo, David S. Goodsell, PDB ID 1iep B. Nagar, W. Bornmann, P. Pellicena, T. Brian Hudson, Catherine Lawson, Maria Voigt and Schindler, D. R. Veach, W. T. Miller, B. Clarkson, J. Kuriyan. Molecular images courtesy of Dr. Hirofumi Suzuki (Osaka University) Christine Zardecki (RCSB PDB). (2002) Crystal structures of the kinase domain of c-Abl in Image of Aequorea victoria based on photo by Sierra Blakely / CC-BY-SA-3.0 complex with the small molecule inhibitors PD173955 and Photo of Corynactis californica © Stan Shebs / Wikimedia Commons / CC- imatinib (STI-571). Cancer Res. 62 : 4236-4243. BY-SA-3.0 / GFDL

August: Tobacco Mosaic Virus December: G Protein-Coupled Receptor PDB ID: 2tmv K. Namba, R. Pattanayek, G. Stubbs. (1989) PDB ID: 3sn6 S. G. Rasmussen, B. T. DeVree, Y. Zou, A. C. Visualization of protein-nucleic acid interactions in a virus. Kruse, K. Y. Chung, T. S. Kobilka, F. S. Thian, P. S. Chae, E. Par - Refined structure of intact tobacco mosaic virus at 2.9 Å don, D. Calinski, J. M. Mathiesen, S. T. Shah, J. A. Lyons, M. resolution by X-ray fiber diffraction. J.Mol.Biol. 208 : Caffrey, S. H. Gellman, J. Steyaert, G. Skiniotis, W. I. Weis, R. K. 307-325. Sunahara, B. K. Kobilka. (2011) Crystal structure of the beta2 adrenergic receptor-Gs protein complex. Nature 477 : 549-555. Inset image courtesy of MRC Laboratory of Molecular Biology Background photo courtesy of Darren Lewis (publicdomainpictures.net) Images courtesy of Dr. Hirofumi Suzuki (Osaka University) Crystallography and the PDB: A Community Resource for Science

In the late 1950s, scientists began to decipher the 3D shapes of proteins at the level of individual atoms. As structures were determined using X-ray crystallography, early computer graphics programs provided interactive views of these macromolecules. The possibilities for science and knowledge seen in these glimpses of myoglobin, 1,2 hemoglobin, 3,4 lysozyme, 5,6 and ribonuclease 7,8 inspired a new field of . The potential research that could be enabled by archiving and sharing data from these experiments moved the scientific community to action. Beginning with the seven structures pictured on the cover –carboxypeptidase, chymotrypsin, cytochrome, hemoglobin (lamprey), lactate dehydrogenase, subtilisin, and trypsin inhibitor – the PDB archive was established in 1971 to provide both a home and an access point for the data produced from these experiments. Today, the PDB contains and supports online access to tens of thousands of biomacromolecular structures determined via X-ray crystallography and other methods. These structures help researchers understand innumerable aspects of biology ranging from biomedicine, agriculture, protein synthesis, health and disease, to biological energy. In 2014, the International Year of Crystallography, the holdings of the PDB archive will reach the 100,000 structure mark. The PDB archive is managed by the Worldwide Protein Data Bank (wwPDB), a consortium of organizations that host deposition, annotation, and distribution centers for PDB data and collaborate on a variety of projects and outreach efforts. The wwPDB partners include: the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and BioMagResBank (BMRB) in the USA, the Protein Data Bank in Europe (PDBe) and the Protein Data Bank Japan (PDBj). The PDB structures highlighted in this calendar illustrate how X-ray crystallography enables our understanding of biology at the atomic level.

wwpdb.org • [email protected] rcsb.org pdbe.org pdbj.org bmrb.wisc.edu